Multiple sequence alignment - TraesCS3A01G424900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G424900 chr3A 100.000 4790 0 0 1 4790 667359728 667354939 0.000000e+00 8846.0
1 TraesCS3A01G424900 chr3A 80.612 98 14 5 4666 4758 743533581 743533678 2.390000e-08 71.3
2 TraesCS3A01G424900 chr3D 94.538 2966 113 16 1470 4405 532175039 532172093 0.000000e+00 4534.0
3 TraesCS3A01G424900 chr3D 89.864 1470 74 28 43 1454 532176474 532175022 0.000000e+00 1820.0
4 TraesCS3A01G424900 chr3D 91.411 326 15 8 4469 4790 532171719 532171403 7.360000e-118 435.0
5 TraesCS3A01G424900 chr3B 91.528 3376 130 51 1470 4790 704328872 704325598 0.000000e+00 4506.0
6 TraesCS3A01G424900 chr3B 93.981 515 22 6 830 1340 704329427 704328918 0.000000e+00 771.0
7 TraesCS3A01G424900 chr3B 100.000 29 0 0 1369 1397 143968471 143968499 2.000000e-03 54.7
8 TraesCS3A01G424900 chr7B 87.342 79 6 2 4457 4531 350458298 350458220 2.370000e-13 87.9
9 TraesCS3A01G424900 chr7D 89.706 68 5 1 4463 4528 461143953 461144020 8.540000e-13 86.1
10 TraesCS3A01G424900 chr5A 89.706 68 5 1 4464 4529 613545309 613545376 8.540000e-13 86.1
11 TraesCS3A01G424900 chr4A 82.000 100 13 5 4666 4760 612401393 612401294 3.970000e-11 80.5
12 TraesCS3A01G424900 chr5D 90.741 54 3 2 4460 4511 491100878 491100931 2.390000e-08 71.3
13 TraesCS3A01G424900 chr2B 100.000 30 0 0 1338 1367 773677680 773677651 6.700000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G424900 chr3A 667354939 667359728 4789 True 8846.0 8846 100.000000 1 4790 1 chr3A.!!$R1 4789
1 TraesCS3A01G424900 chr3D 532171403 532176474 5071 True 2263.0 4534 91.937667 43 4790 3 chr3D.!!$R1 4747
2 TraesCS3A01G424900 chr3B 704325598 704329427 3829 True 2638.5 4506 92.754500 830 4790 2 chr3B.!!$R1 3960

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
28 29 0.184211 ATATGTACCCCCAAACCGCC 59.816 55.0 0.00 0.0 0.00 6.13 F
518 532 0.252558 GACCTCCCACCCCTTCTACA 60.253 60.0 0.00 0.0 0.00 2.74 F
1355 1395 0.477204 TGTACTCCCTCCGATCCGAT 59.523 55.0 0.00 0.0 0.00 4.18 F
1589 1650 0.732538 CGGAAGAAATGTTTGCGCCC 60.733 55.0 4.18 0.0 32.89 6.13 F
3465 3561 1.056660 ACCACGTTCTTCATGGTCCT 58.943 50.0 0.00 0.0 43.40 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1571 1632 0.603065 AGGGCGCAAACATTTCTTCC 59.397 50.000 10.83 0.0 0.0 3.46 R
1954 2018 1.059942 CAAACGAATGAAAAGGCGGC 58.940 50.000 0.00 0.0 0.0 6.53 R
2291 2387 2.294512 GGTGAGCTCCAACAAAAAGAGG 59.705 50.000 12.15 0.0 31.2 3.69 R
3487 3583 1.045407 TACGGGAGCCACATACCATC 58.955 55.000 0.00 0.0 0.0 3.51 R
4364 4478 3.961480 TGTGTACATGAGTGGGAGAAG 57.039 47.619 0.00 0.0 0.0 2.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.849151 AGAATAGAATATGTACCCCCAAACC 58.151 40.000 0.00 0.00 0.00 3.27
26 27 3.570912 AGAATATGTACCCCCAAACCG 57.429 47.619 0.00 0.00 0.00 4.44
27 28 1.951602 GAATATGTACCCCCAAACCGC 59.048 52.381 0.00 0.00 0.00 5.68
28 29 0.184211 ATATGTACCCCCAAACCGCC 59.816 55.000 0.00 0.00 0.00 6.13
29 30 1.206135 TATGTACCCCCAAACCGCCA 61.206 55.000 0.00 0.00 0.00 5.69
30 31 2.674033 GTACCCCCAAACCGCCAC 60.674 66.667 0.00 0.00 0.00 5.01
31 32 3.176433 TACCCCCAAACCGCCACA 61.176 61.111 0.00 0.00 0.00 4.17
32 33 2.540021 TACCCCCAAACCGCCACAT 61.540 57.895 0.00 0.00 0.00 3.21
33 34 2.082836 TACCCCCAAACCGCCACATT 62.083 55.000 0.00 0.00 0.00 2.71
34 35 2.645192 CCCCCAAACCGCCACATTC 61.645 63.158 0.00 0.00 0.00 2.67
35 36 1.905843 CCCCAAACCGCCACATTCA 60.906 57.895 0.00 0.00 0.00 2.57
36 37 1.467678 CCCCAAACCGCCACATTCAA 61.468 55.000 0.00 0.00 0.00 2.69
37 38 0.607620 CCCAAACCGCCACATTCAAT 59.392 50.000 0.00 0.00 0.00 2.57
38 39 1.404047 CCCAAACCGCCACATTCAATC 60.404 52.381 0.00 0.00 0.00 2.67
39 40 1.616620 CAAACCGCCACATTCAATCG 58.383 50.000 0.00 0.00 0.00 3.34
40 41 1.198867 CAAACCGCCACATTCAATCGA 59.801 47.619 0.00 0.00 0.00 3.59
41 42 1.750193 AACCGCCACATTCAATCGAT 58.250 45.000 0.00 0.00 0.00 3.59
50 51 5.221028 GCCACATTCAATCGATACAATTCCA 60.221 40.000 0.00 0.00 0.00 3.53
86 87 3.118261 ACTTCAAAGGACAAGCAGAGTCA 60.118 43.478 5.72 0.00 37.74 3.41
94 95 2.072298 ACAAGCAGAGTCATCGCTTTC 58.928 47.619 10.68 0.00 40.69 2.62
95 96 2.071540 CAAGCAGAGTCATCGCTTTCA 58.928 47.619 10.68 0.00 40.69 2.69
103 104 1.390463 GTCATCGCTTTCAGGTCGTTC 59.610 52.381 0.00 0.00 0.00 3.95
106 107 0.671796 TCGCTTTCAGGTCGTTCTCA 59.328 50.000 0.00 0.00 0.00 3.27
119 120 1.630148 GTTCTCACATCGAGGGAACG 58.370 55.000 0.69 0.00 42.55 3.95
168 170 2.282180 GCAAAGTCTTCGGCCCCA 60.282 61.111 0.00 0.00 0.00 4.96
190 192 1.514678 GCATCACAAACGGCTGGTCA 61.515 55.000 0.00 0.00 0.00 4.02
193 195 0.813610 TCACAAACGGCTGGTCACTG 60.814 55.000 0.00 0.00 0.00 3.66
235 237 3.179265 CCGTGGCGTGAAGTAGCG 61.179 66.667 0.00 0.00 0.00 4.26
253 255 2.301583 AGCGCAACAAACCCCAATTTAT 59.698 40.909 11.47 0.00 0.00 1.40
254 256 2.670905 GCGCAACAAACCCCAATTTATC 59.329 45.455 0.30 0.00 0.00 1.75
255 257 2.920490 CGCAACAAACCCCAATTTATCG 59.080 45.455 0.00 0.00 0.00 2.92
256 258 2.670905 GCAACAAACCCCAATTTATCGC 59.329 45.455 0.00 0.00 0.00 4.58
257 259 3.258228 CAACAAACCCCAATTTATCGCC 58.742 45.455 0.00 0.00 0.00 5.54
258 260 1.474879 ACAAACCCCAATTTATCGCCG 59.525 47.619 0.00 0.00 0.00 6.46
259 261 0.458260 AAACCCCAATTTATCGCCGC 59.542 50.000 0.00 0.00 0.00 6.53
260 262 0.395173 AACCCCAATTTATCGCCGCT 60.395 50.000 0.00 0.00 0.00 5.52
301 303 1.266718 TGAATTGCAGCCAAGTTCGTC 59.733 47.619 0.00 0.00 33.80 4.20
327 329 3.264947 CTGTTTGCCTCGAAGATCATGA 58.735 45.455 0.00 0.00 33.89 3.07
358 360 0.751452 GATCTGGGTACGGGTTCTCC 59.249 60.000 0.00 0.00 0.00 3.71
360 362 0.613853 TCTGGGTACGGGTTCTCCAG 60.614 60.000 5.90 5.90 44.54 3.86
374 376 8.314751 ACGGGTTCTCCAGATATTTATCTAATG 58.685 37.037 0.00 0.00 40.91 1.90
376 378 9.883142 GGGTTCTCCAGATATTTATCTAATGAG 57.117 37.037 0.00 7.04 40.91 2.90
459 472 0.406750 TCCCAACTGAGGTAGGTCGA 59.593 55.000 0.00 0.00 0.00 4.20
471 484 0.394762 TAGGTCGAAGCCGCTCCTTA 60.395 55.000 3.82 0.00 39.27 2.69
472 485 1.227002 GGTCGAAGCCGCTCCTTAG 60.227 63.158 0.00 0.00 35.37 2.18
480 494 1.227674 CCGCTCCTTAGGTCATGCC 60.228 63.158 0.00 0.00 37.58 4.40
512 526 1.539124 GTCAAGACCTCCCACCCCT 60.539 63.158 0.00 0.00 0.00 4.79
518 532 0.252558 GACCTCCCACCCCTTCTACA 60.253 60.000 0.00 0.00 0.00 2.74
519 533 0.546988 ACCTCCCACCCCTTCTACAC 60.547 60.000 0.00 0.00 0.00 2.90
532 548 4.503991 CCCTTCTACACACTTCTTGCTTCT 60.504 45.833 0.00 0.00 0.00 2.85
536 552 7.391148 TTCTACACACTTCTTGCTTCTTTTT 57.609 32.000 0.00 0.00 0.00 1.94
538 554 4.176271 ACACACTTCTTGCTTCTTTTTGC 58.824 39.130 0.00 0.00 0.00 3.68
564 580 1.559368 CCATGCATCAGTTTGGGGAA 58.441 50.000 0.00 0.00 0.00 3.97
609 625 2.413837 GGCGTGCGGTATAGATGAATT 58.586 47.619 0.00 0.00 0.00 2.17
612 628 3.493129 GCGTGCGGTATAGATGAATTCAA 59.507 43.478 13.09 0.00 0.00 2.69
645 661 5.853572 TTCATAGAAGGGGTAACTTGGTT 57.146 39.130 0.00 0.00 0.00 3.67
720 736 1.576356 GCAAATGGTCAAACGGCAAA 58.424 45.000 0.00 0.00 0.00 3.68
732 748 6.160684 GTCAAACGGCAAATAAAATTAGGGT 58.839 36.000 0.00 0.00 0.00 4.34
861 878 1.714899 CTAATTCAGCCCAACCGCCG 61.715 60.000 0.00 0.00 0.00 6.46
879 905 1.708027 GCGCACACATCCGTAGTTC 59.292 57.895 0.30 0.00 0.00 3.01
966 1002 1.746470 CGGAACCCCATTTGACTACC 58.254 55.000 0.00 0.00 0.00 3.18
1187 1223 2.551270 CGAAGATAATGGCGGCGC 59.449 61.111 26.17 26.17 0.00 6.53
1295 1331 8.842280 TGGTACACAATAAAGTCTCGAATTTTT 58.158 29.630 0.00 0.00 30.75 1.94
1349 1385 1.207089 CAGCATTTGTACTCCCTCCGA 59.793 52.381 0.00 0.00 0.00 4.55
1355 1395 0.477204 TGTACTCCCTCCGATCCGAT 59.523 55.000 0.00 0.00 0.00 4.18
1367 1407 2.800544 CCGATCCGATTTAATTGACGCT 59.199 45.455 0.00 0.00 0.00 5.07
1369 1409 3.489416 CGATCCGATTTAATTGACGCTGA 59.511 43.478 0.00 0.00 0.00 4.26
1371 1411 3.591023 TCCGATTTAATTGACGCTGACA 58.409 40.909 0.00 0.00 0.00 3.58
1372 1412 3.997681 TCCGATTTAATTGACGCTGACAA 59.002 39.130 0.00 0.00 0.00 3.18
1374 1414 5.123186 TCCGATTTAATTGACGCTGACAATT 59.877 36.000 17.12 17.12 45.67 2.32
1384 1441 4.033932 TGACGCTGACAATTAATTCGGATG 59.966 41.667 0.00 0.00 0.00 3.51
1390 1447 3.821033 GACAATTAATTCGGATGGGAGGG 59.179 47.826 0.00 0.00 0.00 4.30
1432 1493 5.118990 ACTATATGCTGCCTTTACACACAG 58.881 41.667 0.00 0.00 0.00 3.66
1451 1512 7.560262 ACACACAGCTGATAAGTTCCTAGTATA 59.440 37.037 23.35 0.00 0.00 1.47
1452 1513 8.580720 CACACAGCTGATAAGTTCCTAGTATAT 58.419 37.037 23.35 0.00 0.00 0.86
1453 1514 8.798402 ACACAGCTGATAAGTTCCTAGTATATC 58.202 37.037 23.35 0.00 0.00 1.63
1454 1515 9.019656 CACAGCTGATAAGTTCCTAGTATATCT 57.980 37.037 23.35 0.00 0.00 1.98
1455 1516 9.594936 ACAGCTGATAAGTTCCTAGTATATCTT 57.405 33.333 23.35 0.00 0.00 2.40
1571 1632 4.159879 ACCTCCTAGTCAACATAGAAACCG 59.840 45.833 0.00 0.00 0.00 4.44
1589 1650 0.732538 CGGAAGAAATGTTTGCGCCC 60.733 55.000 4.18 0.00 32.89 6.13
1596 1657 1.627864 AATGTTTGCGCCCTTAAGGT 58.372 45.000 20.22 0.00 38.26 3.50
1611 1672 6.187682 CCCTTAAGGTGTAGTTTCATGGAAT 58.812 40.000 20.22 0.00 0.00 3.01
1612 1673 9.235349 GCCCTTAAGGTGTAGTTTCATGGAATG 62.235 44.444 20.22 0.00 41.85 2.67
1718 1779 8.730093 TGTACTAGCATGGGGTAATAGAATTA 57.270 34.615 0.00 0.00 0.00 1.40
1719 1780 9.333961 TGTACTAGCATGGGGTAATAGAATTAT 57.666 33.333 0.00 0.00 0.00 1.28
1868 1930 3.394674 TCTGTGGTGAACGCTAAATGA 57.605 42.857 0.00 0.00 0.00 2.57
1915 1978 2.174639 TGCCTTTCTTTCCTCCACTTCA 59.825 45.455 0.00 0.00 0.00 3.02
1916 1979 3.181429 TGCCTTTCTTTCCTCCACTTCAT 60.181 43.478 0.00 0.00 0.00 2.57
1945 2009 2.100252 ATGCCAACTTATGCATGTCTGC 59.900 45.455 10.16 6.68 45.96 4.26
1949 2013 9.702434 AATGCCAACTTATGCATGTCTGCTTAC 62.702 40.741 10.16 0.00 46.97 2.34
1959 2023 1.813753 TCTGCTTACATTCGCCGCC 60.814 57.895 0.00 0.00 0.00 6.13
2029 2098 6.335777 AGTAAACGATACATTGTACTCACCC 58.664 40.000 0.00 0.00 0.00 4.61
2031 2100 2.756760 ACGATACATTGTACTCACCCGT 59.243 45.455 0.00 0.63 0.00 5.28
2036 2105 2.895404 ACATTGTACTCACCCGTGTACT 59.105 45.455 0.00 0.00 40.92 2.73
2149 2218 3.065786 TGAATTCGAGCAATGATTCAGGC 59.934 43.478 4.27 5.25 0.00 4.85
2226 2295 9.665719 CAATAAGCCCTGTAAACCATTAAAAAT 57.334 29.630 0.00 0.00 0.00 1.82
2227 2296 9.665719 AATAAGCCCTGTAAACCATTAAAAATG 57.334 29.630 0.00 0.00 0.00 2.32
2228 2297 6.680148 AGCCCTGTAAACCATTAAAAATGT 57.320 33.333 0.00 0.00 0.00 2.71
2231 2300 6.708502 GCCCTGTAAACCATTAAAAATGTTGT 59.291 34.615 0.00 0.00 0.00 3.32
2232 2301 7.095397 GCCCTGTAAACCATTAAAAATGTTGTC 60.095 37.037 0.00 0.00 0.00 3.18
2252 2348 4.082245 TGTCTCAAATCGCAGATCTGTACA 60.082 41.667 23.38 8.54 45.12 2.90
2291 2387 3.367678 GGCAAATGTAAGCATGGCC 57.632 52.632 0.00 0.00 43.95 5.36
2312 2408 2.294512 CCTCTTTTTGTTGGAGCTCACC 59.705 50.000 17.19 0.00 0.00 4.02
2419 2515 5.300969 TGAGAATTCATTTAGCAGCACAC 57.699 39.130 8.44 0.00 0.00 3.82
2463 2559 9.821240 ATTAATGAGATACCTGTCTATGAGAGT 57.179 33.333 0.00 0.00 0.00 3.24
2728 2824 1.195674 GCTCAAACGAACTCAAGGAGC 59.804 52.381 0.00 0.00 39.38 4.70
2898 2994 2.028748 GGACACAAGGCATGCAGAAATT 60.029 45.455 21.36 2.79 0.00 1.82
3038 3134 2.673368 CTGCTTCAAGGGTACGTTCATC 59.327 50.000 0.00 0.00 32.45 2.92
3420 3516 6.314917 AGTCCTTTGTTCCATCCATTTACTT 58.685 36.000 0.00 0.00 0.00 2.24
3450 3546 8.732746 ACTGTTATCCATCTGTTATTTACCAC 57.267 34.615 0.00 0.00 0.00 4.16
3465 3561 1.056660 ACCACGTTCTTCATGGTCCT 58.943 50.000 0.00 0.00 43.40 3.85
3472 3568 5.923114 CACGTTCTTCATGGTCCTATATCAG 59.077 44.000 0.00 0.00 0.00 2.90
3487 3583 6.040955 TCCTATATCAGTAACTCACAGCAAGG 59.959 42.308 0.00 0.00 0.00 3.61
3493 3589 3.838317 AGTAACTCACAGCAAGGATGGTA 59.162 43.478 0.00 0.00 34.98 3.25
3496 3592 2.573462 ACTCACAGCAAGGATGGTATGT 59.427 45.455 0.00 0.00 33.30 2.29
3501 3597 1.133976 AGCAAGGATGGTATGTGGCTC 60.134 52.381 0.00 0.00 34.98 4.70
3511 3607 0.324923 TATGTGGCTCCCGTACTGGT 60.325 55.000 3.00 0.00 35.15 4.00
3536 3632 2.034558 GCCGGTGCATATTTTATGCTGT 59.965 45.455 17.60 0.00 44.79 4.40
3557 3653 1.306296 TGGGGCTTGTTATCCCAGC 59.694 57.895 0.00 0.00 45.04 4.85
3599 3695 2.166829 TGCTTCTCTCTCTGACTGGAC 58.833 52.381 0.00 0.00 0.00 4.02
3640 3736 9.807921 AAGAGATAAAATCCTTCTTTGTTGGTA 57.192 29.630 0.00 0.00 0.00 3.25
3668 3764 4.999950 AGTTGAAGCCTGAAGTATCTTGTG 59.000 41.667 0.00 0.00 0.00 3.33
3670 3766 4.973168 TGAAGCCTGAAGTATCTTGTGTT 58.027 39.130 0.00 0.00 0.00 3.32
3671 3767 4.997395 TGAAGCCTGAAGTATCTTGTGTTC 59.003 41.667 0.00 0.00 0.00 3.18
3703 3799 4.618920 TTTGGACTTCTGGAGGAGTAAC 57.381 45.455 0.00 0.00 0.00 2.50
3901 4005 4.157289 CAGGTATCAATGCTTCAGTTTGCT 59.843 41.667 0.00 0.00 0.00 3.91
3957 4061 7.122799 TCACAGTATAGTGTTAAGAGTGCAGAT 59.877 37.037 10.62 0.00 40.37 2.90
4033 4137 3.005050 TGATGCTTTTCTTGCCTCACTTG 59.995 43.478 0.00 0.00 31.93 3.16
4034 4138 1.682854 TGCTTTTCTTGCCTCACTTGG 59.317 47.619 0.00 0.00 0.00 3.61
4037 4144 3.486383 CTTTTCTTGCCTCACTTGGGTA 58.514 45.455 0.00 0.00 0.00 3.69
4048 4155 5.354513 GCCTCACTTGGGTAAATTTAGAGAC 59.645 44.000 0.00 0.00 0.00 3.36
4095 4202 5.072600 ACCAGTTGACTACCACCTTTATTGA 59.927 40.000 0.00 0.00 0.00 2.57
4139 4246 3.756434 CTCCTGGAATGGCGTTTTTCTTA 59.244 43.478 0.00 0.00 0.00 2.10
4254 4364 4.764679 TTGTTTTAGCTGTATGCCTGTG 57.235 40.909 0.00 0.00 44.23 3.66
4772 5197 8.046708 TGATTTGGTATTGTAGCTGTTGATAGT 58.953 33.333 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.256404 CGGTTTGGGGGTACATATTCTATTCTA 60.256 40.741 0.00 0.00 0.00 2.10
1 2 6.465321 CGGTTTGGGGGTACATATTCTATTCT 60.465 42.308 0.00 0.00 0.00 2.40
2 3 5.704053 CGGTTTGGGGGTACATATTCTATTC 59.296 44.000 0.00 0.00 0.00 1.75
3 4 5.627135 CGGTTTGGGGGTACATATTCTATT 58.373 41.667 0.00 0.00 0.00 1.73
4 5 4.506095 GCGGTTTGGGGGTACATATTCTAT 60.506 45.833 0.00 0.00 0.00 1.98
5 6 3.181452 GCGGTTTGGGGGTACATATTCTA 60.181 47.826 0.00 0.00 0.00 2.10
6 7 2.422377 GCGGTTTGGGGGTACATATTCT 60.422 50.000 0.00 0.00 0.00 2.40
7 8 1.951602 GCGGTTTGGGGGTACATATTC 59.048 52.381 0.00 0.00 0.00 1.75
8 9 1.410507 GGCGGTTTGGGGGTACATATT 60.411 52.381 0.00 0.00 0.00 1.28
9 10 0.184211 GGCGGTTTGGGGGTACATAT 59.816 55.000 0.00 0.00 0.00 1.78
10 11 1.206135 TGGCGGTTTGGGGGTACATA 61.206 55.000 0.00 0.00 0.00 2.29
11 12 2.357446 GGCGGTTTGGGGGTACAT 59.643 61.111 0.00 0.00 0.00 2.29
12 13 3.176433 TGGCGGTTTGGGGGTACA 61.176 61.111 0.00 0.00 0.00 2.90
13 14 2.674033 GTGGCGGTTTGGGGGTAC 60.674 66.667 0.00 0.00 0.00 3.34
14 15 2.082836 AATGTGGCGGTTTGGGGGTA 62.083 55.000 0.00 0.00 0.00 3.69
15 16 3.460478 AATGTGGCGGTTTGGGGGT 62.460 57.895 0.00 0.00 0.00 4.95
16 17 2.603171 AATGTGGCGGTTTGGGGG 60.603 61.111 0.00 0.00 0.00 5.40
17 18 1.467678 TTGAATGTGGCGGTTTGGGG 61.468 55.000 0.00 0.00 0.00 4.96
18 19 0.607620 ATTGAATGTGGCGGTTTGGG 59.392 50.000 0.00 0.00 0.00 4.12
19 20 1.732077 CGATTGAATGTGGCGGTTTGG 60.732 52.381 0.00 0.00 0.00 3.28
20 21 1.198867 TCGATTGAATGTGGCGGTTTG 59.801 47.619 0.00 0.00 0.00 2.93
21 22 1.529226 TCGATTGAATGTGGCGGTTT 58.471 45.000 0.00 0.00 0.00 3.27
22 23 1.750193 ATCGATTGAATGTGGCGGTT 58.250 45.000 0.00 0.00 0.00 4.44
23 24 2.210116 GTATCGATTGAATGTGGCGGT 58.790 47.619 1.71 0.00 0.00 5.68
24 25 2.209273 TGTATCGATTGAATGTGGCGG 58.791 47.619 1.71 0.00 0.00 6.13
25 26 3.942539 TTGTATCGATTGAATGTGGCG 57.057 42.857 1.71 0.00 0.00 5.69
26 27 5.215160 GGAATTGTATCGATTGAATGTGGC 58.785 41.667 1.71 0.00 0.00 5.01
27 28 6.038603 AGTGGAATTGTATCGATTGAATGTGG 59.961 38.462 1.71 0.00 0.00 4.17
28 29 7.019774 AGTGGAATTGTATCGATTGAATGTG 57.980 36.000 1.71 0.00 0.00 3.21
29 30 7.465916 CGAAGTGGAATTGTATCGATTGAATGT 60.466 37.037 1.71 0.00 32.38 2.71
30 31 6.847792 CGAAGTGGAATTGTATCGATTGAATG 59.152 38.462 1.71 0.00 32.38 2.67
31 32 6.017934 CCGAAGTGGAATTGTATCGATTGAAT 60.018 38.462 1.71 0.00 42.00 2.57
32 33 5.293324 CCGAAGTGGAATTGTATCGATTGAA 59.707 40.000 1.71 0.00 42.00 2.69
33 34 4.808895 CCGAAGTGGAATTGTATCGATTGA 59.191 41.667 1.71 0.00 42.00 2.57
34 35 4.808895 TCCGAAGTGGAATTGTATCGATTG 59.191 41.667 1.71 0.00 46.38 2.67
35 36 5.018539 TCCGAAGTGGAATTGTATCGATT 57.981 39.130 1.71 0.00 46.38 3.34
36 37 4.665833 TCCGAAGTGGAATTGTATCGAT 57.334 40.909 2.16 2.16 46.38 3.59
50 51 6.427242 GTCCTTTGAAGTTTCTATTCCGAAGT 59.573 38.462 0.00 0.00 0.00 3.01
60 61 4.526970 TCTGCTTGTCCTTTGAAGTTTCT 58.473 39.130 0.00 0.00 0.00 2.52
86 87 1.272490 TGAGAACGACCTGAAAGCGAT 59.728 47.619 0.00 0.00 0.00 4.58
103 104 1.078759 GTGCGTTCCCTCGATGTGAG 61.079 60.000 0.00 0.00 44.83 3.51
106 107 0.460284 GATGTGCGTTCCCTCGATGT 60.460 55.000 0.00 0.00 0.00 3.06
119 120 2.287188 CGCCATCAATTAGTGGATGTGC 60.287 50.000 11.42 4.51 39.36 4.57
168 170 1.597797 CCAGCCGTTTGTGATGCCAT 61.598 55.000 0.00 0.00 0.00 4.40
190 192 2.118076 CCACCCCCATGCAACAGT 59.882 61.111 0.00 0.00 0.00 3.55
193 195 3.694538 GTGCCACCCCCATGCAAC 61.695 66.667 0.00 0.00 36.65 4.17
218 220 3.179265 CGCTACTTCACGCCACGG 61.179 66.667 0.00 0.00 0.00 4.94
225 227 1.334689 GGGTTTGTTGCGCTACTTCAC 60.335 52.381 22.01 14.76 0.00 3.18
235 237 2.670905 GCGATAAATTGGGGTTTGTTGC 59.329 45.455 0.00 0.00 34.09 4.17
258 260 3.577313 GCCGATCTTCCGCCAAGC 61.577 66.667 0.00 0.00 31.26 4.01
259 261 2.897350 GGCCGATCTTCCGCCAAG 60.897 66.667 0.00 0.00 0.00 3.61
260 262 3.385749 GAGGCCGATCTTCCGCCAA 62.386 63.158 0.00 0.00 0.00 4.52
275 277 0.597568 TTGGCTGCAATTCAACGAGG 59.402 50.000 0.50 0.00 0.00 4.63
301 303 1.939934 TCTTCGAGGCAAACAGTGTTG 59.060 47.619 9.79 5.25 0.00 3.33
327 329 0.179100 CCCAGATCTCGACGCAACAT 60.179 55.000 0.00 0.00 0.00 2.71
416 429 1.406903 GGCTCAAGGGCAAGCATAAT 58.593 50.000 0.00 0.00 40.36 1.28
459 472 0.179000 CATGACCTAAGGAGCGGCTT 59.821 55.000 2.97 0.00 0.00 4.35
480 494 1.073216 CTTGACGAGCGGTGCTACAG 61.073 60.000 0.00 0.00 39.88 2.74
483 497 1.211969 GTCTTGACGAGCGGTGCTA 59.788 57.895 0.00 0.00 39.88 3.49
512 526 7.250569 CAAAAAGAAGCAAGAAGTGTGTAGAA 58.749 34.615 0.00 0.00 0.00 2.10
518 532 4.158394 TCAGCAAAAAGAAGCAAGAAGTGT 59.842 37.500 0.00 0.00 0.00 3.55
519 533 4.675510 TCAGCAAAAAGAAGCAAGAAGTG 58.324 39.130 0.00 0.00 0.00 3.16
538 554 1.460504 AACTGATGCATGGCACTCAG 58.539 50.000 2.46 19.54 43.04 3.35
564 580 1.269831 GCGAGAAGAGTGGAGTGTTGT 60.270 52.381 0.00 0.00 0.00 3.32
592 608 6.857964 CCAAATTGAATTCATCTATACCGCAC 59.142 38.462 9.40 0.00 0.00 5.34
593 609 6.545666 ACCAAATTGAATTCATCTATACCGCA 59.454 34.615 9.40 0.00 0.00 5.69
595 611 8.153479 TCACCAAATTGAATTCATCTATACCG 57.847 34.615 9.40 0.00 0.00 4.02
609 625 7.093377 CCCCTTCTATGAATTTCACCAAATTGA 60.093 37.037 0.15 0.00 41.47 2.57
612 628 6.263754 ACCCCTTCTATGAATTTCACCAAAT 58.736 36.000 0.15 0.00 33.27 2.32
625 641 6.911250 AAAAACCAAGTTACCCCTTCTATG 57.089 37.500 0.00 0.00 0.00 2.23
645 661 7.448161 TCTCCAGAATTTAGCTGACATGAAAAA 59.552 33.333 0.00 0.00 35.39 1.94
685 701 1.506025 TTGCCTTTTGCCCCTTTTCT 58.494 45.000 0.00 0.00 40.16 2.52
686 702 2.340210 TTTGCCTTTTGCCCCTTTTC 57.660 45.000 0.00 0.00 40.16 2.29
687 703 2.585330 CATTTGCCTTTTGCCCCTTTT 58.415 42.857 0.00 0.00 40.16 2.27
691 707 0.321564 GACCATTTGCCTTTTGCCCC 60.322 55.000 0.00 0.00 40.16 5.80
744 760 4.249638 AGCCCTTCTTTTGCATGGTATA 57.750 40.909 0.00 0.00 0.00 1.47
774 790 7.060383 TCCAAGCCTTTTGATCATTTTTGTA 57.940 32.000 0.00 0.00 0.00 2.41
775 791 5.927819 TCCAAGCCTTTTGATCATTTTTGT 58.072 33.333 0.00 0.00 0.00 2.83
776 792 6.864360 TTCCAAGCCTTTTGATCATTTTTG 57.136 33.333 0.00 0.00 0.00 2.44
777 793 7.774625 TCTTTTCCAAGCCTTTTGATCATTTTT 59.225 29.630 0.00 0.00 0.00 1.94
819 835 3.496884 CCGTTGGATTTTCGTTCAGAGAA 59.503 43.478 0.00 0.00 0.00 2.87
821 837 2.412847 GCCGTTGGATTTTCGTTCAGAG 60.413 50.000 0.00 0.00 0.00 3.35
861 878 0.736325 AGAACTACGGATGTGTGCGC 60.736 55.000 0.00 0.00 43.59 6.09
866 883 4.863131 GGAGTAAACAGAACTACGGATGTG 59.137 45.833 0.00 0.00 0.00 3.21
868 885 4.081862 TGGGAGTAAACAGAACTACGGATG 60.082 45.833 0.00 0.00 0.00 3.51
871 888 3.582780 GTGGGAGTAAACAGAACTACGG 58.417 50.000 0.00 0.00 0.00 4.02
872 889 3.240069 CGTGGGAGTAAACAGAACTACG 58.760 50.000 0.00 0.00 0.00 3.51
873 890 2.991866 GCGTGGGAGTAAACAGAACTAC 59.008 50.000 0.00 0.00 0.00 2.73
879 905 2.388232 GCGGCGTGGGAGTAAACAG 61.388 63.158 9.37 0.00 0.00 3.16
1038 1074 2.475466 GGATACCGACGAGGACGCA 61.475 63.158 8.56 0.00 45.00 5.24
1052 1088 2.552819 CGCGAGCCGGAAGAGGATA 61.553 63.158 5.05 0.00 0.00 2.59
1215 1251 2.511600 GCGAACGACATCCCCAGG 60.512 66.667 0.00 0.00 0.00 4.45
1236 1272 4.471726 CGTACCCGCGCGAGAACT 62.472 66.667 34.63 4.38 0.00 3.01
1265 1301 3.930848 GAGACTTTATTGTGTACCACCGG 59.069 47.826 0.00 0.00 32.73 5.28
1267 1303 4.813027 TCGAGACTTTATTGTGTACCACC 58.187 43.478 0.00 0.00 32.73 4.61
1304 1340 5.849510 ACTAGCGCAACCATGTATGTAATA 58.150 37.500 11.47 0.00 0.00 0.98
1306 1342 4.116961 GACTAGCGCAACCATGTATGTAA 58.883 43.478 11.47 0.00 0.00 2.41
1307 1343 3.491964 GGACTAGCGCAACCATGTATGTA 60.492 47.826 11.47 0.00 0.00 2.29
1308 1344 2.550978 GACTAGCGCAACCATGTATGT 58.449 47.619 11.47 0.00 0.00 2.29
1309 1345 1.867233 GGACTAGCGCAACCATGTATG 59.133 52.381 11.47 0.00 0.00 2.39
1310 1346 1.484653 TGGACTAGCGCAACCATGTAT 59.515 47.619 11.47 0.00 0.00 2.29
1349 1385 4.188462 TGTCAGCGTCAATTAAATCGGAT 58.812 39.130 0.00 0.00 0.00 4.18
1367 1407 4.460263 CCTCCCATCCGAATTAATTGTCA 58.540 43.478 5.17 0.00 0.00 3.58
1369 1409 3.461831 TCCCTCCCATCCGAATTAATTGT 59.538 43.478 5.17 0.00 0.00 2.71
1371 1411 3.722101 ACTCCCTCCCATCCGAATTAATT 59.278 43.478 0.00 0.00 0.00 1.40
1372 1412 3.327439 ACTCCCTCCCATCCGAATTAAT 58.673 45.455 0.00 0.00 0.00 1.40
1374 1414 2.489528 ACTCCCTCCCATCCGAATTA 57.510 50.000 0.00 0.00 0.00 1.40
1384 1441 3.653835 AAGAAAATGCTACTCCCTCCC 57.346 47.619 0.00 0.00 0.00 4.30
1571 1632 0.603065 AGGGCGCAAACATTTCTTCC 59.397 50.000 10.83 0.00 0.00 3.46
1589 1650 7.921786 TCATTCCATGAAACTACACCTTAAG 57.078 36.000 0.00 0.00 36.11 1.85
1611 1672 5.626142 TCCAATAGGCACACTAAACTTTCA 58.374 37.500 0.00 0.00 34.79 2.69
1612 1673 6.349363 CCTTCCAATAGGCACACTAAACTTTC 60.349 42.308 0.00 0.00 34.79 2.62
1681 1742 6.163476 CCATGCTAGTACAAGTAAACAGTCA 58.837 40.000 0.00 0.00 0.00 3.41
1718 1779 9.936329 AAACCCCATGTTATTTCATCTACTTAT 57.064 29.630 0.00 0.00 35.67 1.73
1720 1781 9.762381 TTAAACCCCATGTTATTTCATCTACTT 57.238 29.630 0.00 0.00 35.67 2.24
1721 1782 9.936329 ATTAAACCCCATGTTATTTCATCTACT 57.064 29.630 0.00 0.00 35.67 2.57
1868 1930 8.362639 AGCACATTCAACAGTTCAATTTTAGAT 58.637 29.630 0.00 0.00 0.00 1.98
1915 1978 4.467082 TGCATAAGTTGGCATTGGAAAGAT 59.533 37.500 0.00 0.00 34.58 2.40
1916 1979 3.831333 TGCATAAGTTGGCATTGGAAAGA 59.169 39.130 0.00 0.00 34.58 2.52
1945 2009 1.466950 TGAAAAGGCGGCGAATGTAAG 59.533 47.619 12.98 0.00 0.00 2.34
1949 2013 1.548986 GAATGAAAAGGCGGCGAATG 58.451 50.000 12.98 0.00 0.00 2.67
1954 2018 1.059942 CAAACGAATGAAAAGGCGGC 58.940 50.000 0.00 0.00 0.00 6.53
1959 2023 3.735746 GGGAACTGCAAACGAATGAAAAG 59.264 43.478 0.00 0.00 0.00 2.27
2031 2100 5.984323 TGAAACGCAAATGTGTAGTAGTACA 59.016 36.000 6.31 6.31 37.87 2.90
2036 2105 6.370166 TGATCATGAAACGCAAATGTGTAGTA 59.630 34.615 0.00 0.00 37.87 1.82
2149 2218 1.368641 TGACCGGATGCAATCTTTCG 58.631 50.000 9.46 0.00 44.71 3.46
2201 2270 9.665719 CATTTTTAATGGTTTACAGGGCTTATT 57.334 29.630 0.00 0.00 0.00 1.40
2226 2295 3.681417 CAGATCTGCGATTTGAGACAACA 59.319 43.478 10.38 0.00 0.00 3.33
2227 2296 3.681897 ACAGATCTGCGATTTGAGACAAC 59.318 43.478 22.83 0.00 0.00 3.32
2228 2297 3.930336 ACAGATCTGCGATTTGAGACAA 58.070 40.909 22.83 0.00 0.00 3.18
2231 2300 4.718940 TGTACAGATCTGCGATTTGAGA 57.281 40.909 22.83 0.00 0.00 3.27
2232 2301 5.045872 TGATGTACAGATCTGCGATTTGAG 58.954 41.667 22.83 0.00 0.00 3.02
2252 2348 3.012518 CAAAGATTCCTTCACCGCTGAT 58.987 45.455 0.00 0.00 0.00 2.90
2291 2387 2.294512 GGTGAGCTCCAACAAAAAGAGG 59.705 50.000 12.15 0.00 31.20 3.69
2312 2408 9.388506 AGATATACAAGGAATGTCAACAGAAAG 57.611 33.333 0.00 0.00 42.70 2.62
2419 2515 2.783828 ATACGATGAAGCGTCCTCAG 57.216 50.000 0.00 1.78 44.39 3.35
2463 2559 7.454553 AGAAGAGTATTCAGGAGTAGGACTA 57.545 40.000 0.00 0.00 0.00 2.59
2728 2824 6.066054 TCTCATGCTAAGACTAATCTCACG 57.934 41.667 0.00 0.00 32.34 4.35
2898 2994 7.841729 ACAAGGAAATCTATAAGAGTCCTCAGA 59.158 37.037 10.72 0.00 40.11 3.27
3038 3134 8.543774 CAAGAGTAATTTTGAGCGATAAGGTAG 58.456 37.037 0.00 0.00 0.00 3.18
3228 3324 2.675844 CCAAGCAATTGCCACAATCATG 59.324 45.455 26.45 12.07 43.38 3.07
3420 3516 8.877864 AAATAACAGATGGATAACAGTTTCCA 57.122 30.769 15.43 15.43 45.69 3.53
3450 3546 6.090483 ACTGATATAGGACCATGAAGAACG 57.910 41.667 0.00 0.00 0.00 3.95
3465 3561 7.436933 CATCCTTGCTGTGAGTTACTGATATA 58.563 38.462 0.00 0.00 0.00 0.86
3472 3568 3.059352 ACCATCCTTGCTGTGAGTTAC 57.941 47.619 0.00 0.00 0.00 2.50
3487 3583 1.045407 TACGGGAGCCACATACCATC 58.955 55.000 0.00 0.00 0.00 3.51
3493 3589 1.198759 AACCAGTACGGGAGCCACAT 61.199 55.000 19.63 0.00 40.22 3.21
3496 3592 1.675219 GAAACCAGTACGGGAGCCA 59.325 57.895 19.63 0.00 40.22 4.75
3501 3597 2.812178 CGGCGAAACCAGTACGGG 60.812 66.667 10.83 10.83 40.22 5.28
3511 3607 3.793801 GCATAAAATATGCACCGGCGAAA 60.794 43.478 9.30 0.00 45.35 3.46
3536 3632 1.306296 GGGATAACAAGCCCCAGCA 59.694 57.895 0.00 0.00 43.56 4.41
3557 3653 2.859165 TGGAAGTAAGCCAGTCAAGG 57.141 50.000 0.00 0.00 0.00 3.61
3599 3695 3.241067 TCTCTTCCGTAAAATGGTCCG 57.759 47.619 0.00 0.00 0.00 4.79
3610 3706 7.168905 ACAAAGAAGGATTTTATCTCTTCCGT 58.831 34.615 0.00 0.00 37.32 4.69
3612 3708 8.246871 CCAACAAAGAAGGATTTTATCTCTTCC 58.753 37.037 0.00 0.00 37.32 3.46
3640 3736 2.919228 ACTTCAGGCTTCAACTTCGTT 58.081 42.857 0.00 0.00 0.00 3.85
3653 3749 9.612620 GTTTATTTGAACACAAGATACTTCAGG 57.387 33.333 0.00 0.00 0.00 3.86
3668 3764 7.438160 CCAGAAGTCCAAAAGGTTTATTTGAAC 59.562 37.037 0.83 0.00 39.56 3.18
3670 3766 6.836527 TCCAGAAGTCCAAAAGGTTTATTTGA 59.163 34.615 0.83 0.00 39.56 2.69
3671 3767 7.049799 TCCAGAAGTCCAAAAGGTTTATTTG 57.950 36.000 0.00 0.00 37.48 2.32
3703 3799 7.546316 TGAGGCAAACATCAAATTCAACATATG 59.454 33.333 0.00 0.00 0.00 1.78
3901 4005 9.237187 TGCACCTTGAGAACAAAAATATATACA 57.763 29.630 0.00 0.00 35.49 2.29
3917 4021 1.233019 CTGTGACCTTGCACCTTGAG 58.767 55.000 0.00 0.00 37.99 3.02
3957 4061 0.250124 CACAGGTGGCAGTTAACCGA 60.250 55.000 0.88 0.00 41.61 4.69
4033 4137 8.788325 ACACTGTATTGTCTCTAAATTTACCC 57.212 34.615 0.00 0.00 0.00 3.69
4048 4155 6.347725 GGTCTGCACTCTTTAACACTGTATTG 60.348 42.308 0.00 0.00 0.00 1.90
4060 4167 2.171448 AGTCAACTGGTCTGCACTCTTT 59.829 45.455 0.00 0.00 0.00 2.52
4095 4202 8.767436 AGGAGAAAGATTAGAAGAGCATAACTT 58.233 33.333 0.00 0.00 0.00 2.66
4139 4246 4.685924 CAAAAAGATTGCACAACTGAGGT 58.314 39.130 0.00 0.00 0.00 3.85
4364 4478 3.961480 TGTGTACATGAGTGGGAGAAG 57.039 47.619 0.00 0.00 0.00 2.85
4439 4813 4.741321 TGTTACGGGGTATTTCACTAGG 57.259 45.455 0.00 0.00 0.00 3.02


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.